Oligo Vendor Format Converter - IDT, Twist, GenScript & Dynegene

Upload your FASTA file or paste sequences directly. Select "IDT" as your vendor, choose your desired scale (25nm-10um), select purification method (Desalting, HPLC, or PAGE), and configure any modifications needed. The tool automatically extracts sequence names from FASTA headers and validates sequences. Click convert and download the Excel file ready for direct upload to IDT's ordering portal. The output includes Name, Sequence, Scale, and Purification columns matching IDT's oPools requirements.

IDT oPools format uses Excel with columns: Name, Sequence, Scale, Purification. Scales range from 25nm to 10um with multiple purification options. Twist Bioscience uses CSV format with Name, Sequence, and Length columns. The Length field is automatically calculated. Twist supports much larger pools (up to 350,000 oligos vs IDT's 10,000) and uses silicon-based synthesis for higher uniformity. IDT offers more purification and modification options. Choose based on your pool size, modification needs, and vendor relationship.

You can upload three types of input formats: FASTA files (.fasta, .fa) with standard multi-sequence format using ">" headers, CSV files (.csv) with Name,Sequence columns (header row is optional), or plain text files (.txt) for single sequences. The tool automatically detects the format based on content structure, so you don't need to specify the format manually. Maximum file size is limited by browser memory, but typically handles up to 10,000 sequences efficiently.

You can convert up to 10,000 sequences in a single batch. This limit ensures optimal browser performance and quick processing. For larger orders, consider splitting your sequences into multiple batches. The tool processes sequences client-side, so processing time depends on your computer's performance. Most batches of 1,000 sequences or fewer process in under 5 seconds.

Yes, you can specify modifications for GenScript and IDT formats. For GenScript, use the modification field with structured syntax: "5'-modification / 3'-modification / Internal-position-modification". Common modifications include 5' Phosphate, 3' Biotin, phosphorothioate bonds, and fluorophores. For IDT, modifications can be added in the export file. Twist Bioscience requires contacting them directly for modified oligos. Always verify vendor capabilities for specific modifications at your selected scale before ordering.

The tool performs comprehensive validation: sequence length checks (warns for sequences <15 nt or >300 nt per vendor minimums—shorter sequences may not meet synthesis requirements, longer sequences may require Ultramer or special handling), character validation (ensures only valid DNA/RNA characters: ATCGURYMKSWBDHVN), GC content calculation for quality assessment, and flags potential synthesis issues. Errors indicate critical problems that may prevent synthesis, while warnings highlight potential concerns you should review before ordering.

No, we never store your sequences. All processing happens entirely in your browser (client-side). Your sequences are never uploaded to our servers and remain completely private. This ensures maximum privacy and security for your research data. You can verify this by checking your browser's network tab - no data is sent to our servers during conversion.

The tool calculates GC% for all sequences and flags potential issues. Recommended ranges: 20-80% GC for Twist Bioscience (optimal synthesis), 30-70% GC for IDT and GenScript (standard synthesis). Sequences with extreme GC content (<20% or >80%) may have reduced synthesis efficiency, higher error rates, or require special handling. For sequences outside recommended ranges, consider: redesigning with synonymous codons, adding GC-balancing flanking sequences, or contacting the vendor for feasibility assessment before ordering.

Common rejection reasons and fixes: 1) File encoding issue - ensure Excel files are saved as .xlsx (not .xls) and CSV files use UTF-8 encoding without BOM. 2) Column header mismatch - verify column names exactly match vendor requirements (case-sensitive). 3) Special characters in sequence names - use only alphanumeric characters, underscores, and hyphens. 4) Invalid sequence characters - check for lowercase letters, spaces, or non-IUPAC codes. 5) Empty cells - ensure all required fields (Name, Sequence, Scale) are populated. Re-download from our tool if issues persist, as it generates properly formatted files.

Ambiguity codes (IUPAC degenerate bases) are generally NOT synthesized as mixed bases by standard oligo vendors. The tool accepts ambiguity codes for validation purposes, but most vendors will either: 1) Reject sequences containing them, or 2) Require you to specify exact base composition. For degenerate oligonucleotides, you need to either: convert ambiguity codes to specific sequences (e.g., R → separate A and G oligos), order from specialized vendors offering mixed-base synthesis, or contact your vendor for custom degenerate oligo services. IDT offers "Hand Mix" options for some degenerate positions.

Verification checklist: 1) Open the downloaded Excel/CSV file and spot-check 5-10 sequences against your original input to ensure sequences match exactly. 2) Verify all sequence names are present and correctly formatted. 3) Check that Scale and Purification columns contain your selected values. 4) For Twist format, confirm the Length column matches actual sequence lengths. 5) Look for any empty cells or error values (#N/A, #REF). 6) Ensure total sequence count matches your input (check last row number). 7) For large pools, import back into our Batch Sequence QC tool for final validation before vendor submission.

Post-synthesis workflow: 1) Use our Molecular Weight Calculator to determine proper resuspension volumes based on your ordered scale (e.g., 100 nmol scale). 2) Resuspend oligos in nuclease-free water or TE buffer to desired concentration (typically 100 µM stock). 3) For oligo pools, perform NGS quality control to verify pool composition and uniformity. 4) Aliquot stocks to avoid freeze-thaw cycles (store at -20°C or -80°C). 5) For CRISPR libraries or functional assays, validate a subset of sequences by Sanger sequencing. 6) Document lot numbers and synthesis dates for traceability. 7) Refer to vendor-provided QC reports (mass spec, OD260 measurements) to verify synthesis quality.